Some relatively recent medical research has shed light on why the rhythm method may be ineffective for some women:

Conventional wisdom, and decades of medical and biological knowledge, has always held that women ovulate (i.e. produce an ovum that can be fertilised by sperm) around the middle of their (approximately) 28 day menstrual cycle. Researchers have now found that some women (around 10% of their relatively small sample population of 63 women) can actually ovulate more than once.

Now for these women the rhythm method is bound to be unsuccessful for the following reason: the rhythm method is based around having sex when the woman is not ovulating. There is currently no good way, short of a gynaecological examination, to tell whether a woman is ovulating or not. As a consequence, the rhythm method relies on the assumption that a woman ovulates exactly once each menstrual cycle, and always around the 14th day. If this research is correct1, then this assumption is not always valid, and so the rhythm method is very fallible.

Footnotes:1 Basing medical knowledge upon a sample population of only 63 women (of 124 in the medical trial itself) is always dangerous, and should be taken with copious amounts of salt.